$file=$ARGV[0];
chomp($file);
$input_r2=$ARGV[1];
chomp($input_r2);
$output_r2=$ARGV[2];
chomp($output_r2);
open(BUFF,$file) or die "no $file exists\n";
while(<BUFF>)
{
	chomp($_);
	$hash{$_}=1;
}
open(BUFF,$input_r2) or die "no $input_r2 exists\n";
open(WRBUFF,">$output_r2") or die "no $output_r2 exists\n";
$line=<BUFF>;
chomp($line);
$sign="GBM_";
$line=~ s/ /_/g;
$line=~ s/^/$sign/g;
$line=~ s/\t/\t$sign/g;	
print WRBUFF $line;
$fil="$sign"."INDICATOR";
print WRBUFF "\t$fil\n";
while(<BUFF>)
{
	chomp($_);
	@a=split("\t",$_);
	#print $a[0]."\n";
	if(exists($hash{$a[0]}))
	{
		#print "sucess\n";
		print WRBUFF $_."\tINPUT\n";
	}
	else
	{
		print WRBUFF $_."\tIMPUTED\n";
	}
}
